Single-cell RNA-seq (scRNA-seq) is increasingly used in a range of biomedical studies. Nonetheless, current RNA-seq analysis tools are not specifically designed to efficiently process scRNA-seq data due to their limited scalability. Here researchers from the Victor Chang Cardiac Research Institute ...
Read More »SAMSA – a comprehensive metatranscriptome analysis pipeline
Although metatranscriptomics-the study of diverse microbial population activity based on RNA-seq data-is rapidly growing in popularity, there are limited options for biologists to analyze this type of data. Current approaches for processing metatranscriptomes rely on restricted databases and a dedicated ...
Read More »ChloroSeq – an organelle RNA-Seq bioinformatics pipeline
Online sequence repositories are teeming with RNA sequencing (RNA-Seq) data from a wide range of eukaryotes. Although most of these data sets contain large numbers of organelle-derived reads, researchers tend to ignore these data, focusing instead on the nuclear-derived transcripts. ...
Read More »Phenotype prediction from alternative splicing and gene expression data
A central task of bioinformatics is to develop sensitive and specific means of providing medical prognoses from biomarker patterns. Common methods to predict phenotypes in RNA-Seq datasets utilize machine learning algorithms trained via gene expression. Isoforms, however, generated from alternative ...
Read More »An open RNA-Seq data analysis pipeline/tutorial with an example of reprocessing data from a recent Zika virus study
RNA-seq analysis is becoming a standard method for global gene expression profiling. However, open and standard pipelines to perform RNA-seq analysis by non-experts remain challenging due to the large size of the raw data files and the hardware requirements for ...
Read More »A Novel Analytical Strategy to Identify Fusion Transcripts between Repetitive Elements and Protein Coding-Exons Using RNA-Seq
Repetitive elements (REs) comprise 40–60% of the mammalian genome and have been shown to epigenetically influence the expression of genes through the formation of fusion transcript (FTs). Researchers from the National Institute of Environmental Health Sciences previously showed that an intracisternal ...
Read More »Combinatorial Analysis Performed Using gSELEX-Seq and RNA-Seq
For identifying the genes that are regulated by a transcription factor (TF), Nagoya University researchers have established an analytical pipeline that combines genomic systematic evolution of ligands by exponential enrichment (gSELEX)-Seq and RNA-Seq. Here, SELEX was used to select DNA ...
Read More »aRNApipe – A balanced, efficient and distributed pipeline for processing RNA-seq data in high performance computing environments
The wide range of RNA-seq applications and their high computational needs require the development of pipelines orchestrating the entire workflow and optimizing usage of available computational resources. Researchers at the HudsonAlpha Institute for Biotechnology have developed aRNApipe, a project-oriented pipeline ...
Read More »The exon quantification pipeline (EQP) – a comprehensive approach to the quantification of gene, exon and junction expression from RNA-seq data
The quantification of transcriptomic features is the basis of the analysis of RNA-seq data. Researchers at the Novartis Institutes for Biomedical Research have developed an integrated alignment workflow and a simple counting-based approach to derive estimates for gene, exon and ...
Read More »SARTools – A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data
Several R packages exist for the detection of differentially expressed genes from RNA-Seq data. The analysis process includes three main steps, namely normalization, dispersion estimation and test for differential expression. Quality control steps along this process are recommended but not ...
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